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De Wolfe TJ, Wright ES. Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis. BMC Microbiol 2023; 23:107. [PMID: 37076812 PMCID: PMC10114302 DOI: 10.1186/s12866-023-02851-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/04/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND The development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of microbial ecology. However, the variety of methodologies used among amplicon sequencing workflows leads to uncertainty about best practices as well as reproducibility and replicability among microbiome studies. Using a bacterial mock community composed of 37 soil isolates, we performed a comprehensive methodological evaluation of workflows, each with a different combination of methodological factors spanning sample preparation to bioinformatic analysis to define sources of artifacts that affect coverage, accuracy, and biases in the resulting compositional profiles. RESULTS Of the workflows examined, those using the V4-V4 primer set enabled the highest level of concordance between the original mock community and resulting microbiome sequence composition. Use of a high-fidelity polymerase, or a lower-fidelity polymerase with an increased PCR elongation time, limited chimera formation. Bioinformatic pipelines presented a trade-off between the fraction of distinct community members identified (coverage) and fraction of correct sequences (accuracy). DADA2 and QIIME2 assembled V4-V4 reads amplified by Taq polymerase resulted in the highest accuracy (100%) but had a coverage of only 52%. Using mothur to assemble and denoise V4-V4 reads resulted in a coverage of 75%, albeit with marginally lower accuracy (99.5%). CONCLUSIONS Optimization of microbiome workflows is critical for accuracy and to support reproducibility and replicability among microbiome studies. These considerations will help reveal the guiding principles of microbial ecology and impact the translation of microbiome research to human and environmental health.
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Affiliation(s)
- Travis J. De Wolfe
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, 450 Technology Drive Rm. 426, Pittsburgh, PA 15219 USA
- Department of Pediatrics, BC Children’s Hospital Research Institute, University of British Columbia, 4480 Oak Street Rm. 208B, Vancouver, BC V6H 4E4 Canada
- Gut4Health, BC Children’s Hospital Research Institute, University of British Columbia, 950 West 28th Avenue Rm. 211, Vancouver, BC V5Z 4H4 Canada
| | - Erik S. Wright
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, 450 Technology Drive Rm. 426, Pittsburgh, PA 15219 USA
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Kamira B, Shi LL, Fan LM, Zhang C, Zheng Y, Song C, Meng SL, Hu GD, Bing XW, Chen ZJ, Xu P. Methane-generating ammonia oxidizing nitrifiers within bio-filters in aquaculture tanks. AMB Express 2018; 8:140. [PMID: 30155810 PMCID: PMC6113197 DOI: 10.1186/s13568-018-0668-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 08/17/2018] [Indexed: 11/10/2022] Open
Abstract
The discovery of aerobic and anammox bacteria capable of generating methane in bio-filters in freshwater aquaculture systems is generating interest in studies to understand the activity, diversity, distribution and roles of these environmental bacteria. In this study, we used microbial enrichment of bio-filters to assess their effect on water quality. Profiles of ammonia-oxidizing bacterial communities generated using nested PCR methods and DGGE were used to assess the expression of 16S rRNA genes using DNA sequencing. Five dominant ammonia-oxidizing bacterial strains-clones; KB.13, KB.15, KB.16, KB.17 and KB.18-were isolated and identified by phylogenetic analysis as environmental samples closely related to genera Methylobacillus, Stanieria, Nitrosomonas, and Heliorestis. The methyl ammonia-oxidizing microbes thereby found suggest a biochemical pathway involving electron donors and carbon sources, and all strains were functional in freshwater aquaculture systems. Environmental parameters including TN (2.69-20.43); COD (9.34-31.47); NH4+-N (0.44-11.78); NO2-N (0.00-3.67); NO3-N (0.05-1.82), mg/L and DO (1.47-10.31 µg/L) assessed varied in the ranges in the different tanks. Principal component analysis revealed that these water quality parameters significantly influenced the ammonia oxidizing microbial community composition. Temperature rises to about 40 °C significantly affected environmental characteristics-especially DO, TN and NH4+-N-and directly or indirectly affected the microbial communities. Although the nested PCR design was preferred due to its high sensitivity for amplifying specific DNA regions, a more concise method is recommended, as an equimolar mixture of degenerate PCR primer pairs, CTO189f-GC and CTO654r, never amplified only 16S rRNA of ammonia-oxidizing bacteria.
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Affiliation(s)
- Barry Kamira
- Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 Jiangsu People’s Republic of China
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Present Address: Freshwater Fisheries Resources Center (FFRC), Chinese Academy of Fisheries Sciences (CAFs), Wuxi, People’s Republic of China
| | - Lei Lei Shi
- Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 Jiangsu People’s Republic of China
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
| | - Li Min Fan
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Cong Zhang
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Yao Zheng
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Chao Song
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Shun Long Meng
- Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 Jiangsu People’s Republic of China
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Geng Dong Hu
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Xu Wen Bing
- Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 Jiangsu People’s Republic of China
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Zhang Jia Chen
- Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 Jiangsu People’s Republic of China
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
| | - Pao Xu
- Nanjing Agricultural University, 1 Weigang, Nanjing, 210095 Jiangsu People’s Republic of China
- Wuxi Fisheries College, 9 East Shan Shui Road, Binhu District, Wuxi, 214081 Jiangsu People’s Republic of China
- Key Laboratory of Freshwater Fisheries Eco-Environment Monitoring Center of Lower Reaches of Yantze River, Ministry of Agriculture; Fishery Environmental Protection Department, Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), Wuxi, Jiangsu People’s Republic of China
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Kim TG, Kim SH, Cho KS. Effects of ultrasonic pretreatment on quantity and composition of bacterial DNA recovered from granular activated carbon used for drinking water treatment. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2014; 49:609-616. [PMID: 24410692 DOI: 10.1080/10934529.2014.859469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Effects of ultrasonic pretreatment on bacterial DNA recovery from granular activated carbon (GAC) were investigated. GAC (Calgon F400), biologically activated, was sampled from an actual drinking water plant. Different ultrasonic energy densities (0-400 J·cm(-3)) were applied with agitation (250 rpm for 30 min), and recovered bacterial DNA was quantified using quantitative PCR. Energy density was linearly correlated with the concentration of carbon fines produced from GAC during ultrasonication. Ultrasonication alone had no effect on DNA recovery at ≤60 J·cm(-3), but a strongly adverse effect at >67 J·cm(-3) due to the produced carbon fines. Agitation along with ultrasonication strongly enhanced the bacterial DNA recovery when ≤40 J·cm(-3) was applied, although it did not affect the production of carbon fines. Ribosomal tag pyrosequencing was used to compare recovered bacterial communities (0, 20 and 30 J·cm(-3) with or without agitation). Ultrasonication allowed for obtaining a more diverse and richer bacterial community from GAC, compared with the control. Agitation did not show a positive effect on community organization (richness and diversity). Consistently, canonical correspondence analysis indicated that the energy density was associated with the relative abundances of particular bacterial members (P < 0.05), while agitation did not. Correspondence analysis revealed that the recovered bacterial communities were grouped according to the applied energy densities. In conclusion, ultrasonication and agitation influence the recovered DNA in quality and quantity, respectively, and carbon fines as a by-product by ultrasonication interfere with the DNA recovery.
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Affiliation(s)
- Tae Gwan Kim
- a Global Top5 Research Program, Department of Environmental Science and Engineering , Ewha Womans University , Daehyun-dong , Seodaemun-gu , Seoul , Republic of Korea
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Zhang D, Li W, Huang X, Qin W, Liu M. Removal of ammonium in surface water at low temperature by a newly isolated Microbacterium sp. strain SFA13. BIORESOURCE TECHNOLOGY 2013; 137:147-152. [PMID: 23584414 DOI: 10.1016/j.biortech.2013.03.094] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/09/2013] [Accepted: 03/13/2013] [Indexed: 06/02/2023]
Abstract
The strain SFA13, isolated from Songhua River, demonstrates ability to convert ammonium to nitrogen under aerobic conditions at low temperature. On the basis of 16S rRNA gene sequence, the strain SFA13 was a species in genera Microbacterium. The isolate showed unusual ability of autotrophic nitrification with the ratio of 0.11 mg NH4(+)-N/L/h at 5°C. Ammonium was consumed by the strain SFA13 with the biodegradation of organic carbon and without nitrite or nitrate accumulation. NO3(-)-N or NO2(-)-N was reduced by the strain SFA13. The denitrification ratio was 0.24mgNO3(-)-N/L/h. Hydroxylamine oxidase, nitrite reductase and nitrate reductase were detectable. The putative nitrogen removal process by the strain SFA13 was as follows: NH4(+)→NH2OH→NO2(-)→NO3(-), then NO3(-)→NO2(-)→N2. Biological activated carbon attached with the strain SFA13 could effectively remove ammonium in surface water with the rate of 2.68±0.27-3.16±0.25 mg NH4(+)-N/L/h at C/N 2-10, temperature 10°C, and DO>5.2 mg/L.
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Affiliation(s)
- Duoying Zhang
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
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